A lithographic apparatus includes a liquid confinement system to confine liquid in a space between a final element of a projection system and a substrate, and a first and a second substrate stage that are configured to mutually cooperate in order to perform a joint movement for bringing the lithographic apparatus from a first configuration, in which the liquid is confined between a first substrate held by the first substrate stage and the final element, towards a second configuration, in which the liquid is confined between a second substrate held by the second substrate stage and the final element, such that during the joint movement the liquid is essentially confined within the space with respect to the final element. The apparatus also includes a position measurement system configured to at least during the joint movement measure the position of the first and second substrate stages.